predictExonsTerminal

<code>IRanges</code> of candidate internal exons

candidates

<code>IRangesList</code> with exonic regions from alignments

frag_exonic

<code>IRangesList</code> with introns implied by spliced
alignments

frag_intron

Minimum relative coverage required for exon prediction

relCov

Integer specifiying minimum anchor length

min_anchor

Character string indicating whether terminal exons
should be identified to the left (<dquote>exon_L</dquote>) or right
(<dquote>exon_R</dquote>) of provided splice sites

type

Logical indicating whether counts of
compatible fragments should be included in metadata column
<dquote>N</dquote>

include_counts

Logical indicating whether coverage for each
exon should be retained as an <code>RleList</code> in metadata
column <dquote>coverage</dquote>. This allows filtering of features
using more stringent criteria after the initial prediction.

retain_coverage

Identify terminal exons based on candidate terminal exons and
compatible read coverage.

internal

SGSeq is a software package for analyzing splice events from
	     RNA-seq data. Input data are sequence reads mapped to a reference
	     genome in BAM format. Genes are represented as a genome-wide
	     splice graph, which can be obtained from existing annotation or
	     can be predicted from the data. Splice events are identified
	     from the graph and are quantified locally using structurally
	     compatible reads at the start or end of each splice variant.
	     The package includes functions for splice event prediction,
	     quantification, visualization and interpretation.

Leonard Goldstein

SGSeq

Splice event prediction and quantification from RNA-seq data

predictExonsTerminal function

Character string indicating whether terminal exons
should be identified to the left (<dQuote>exon_L</dQuote>) or right
(<dQuote>exon_R</dQuote>) of provided splice sites

Logical indicating whether counts of
compatible fragments should be included in metadata column
<dQuote>N</dQuote>

Logical indicating whether coverage for each
exon should be retained as an <code>RleList</code> in metadata
column <dQuote>coverage</dQuote>. This allows filtering of features
using more stringent criteria after the initial prediction.

predictExonsTerminal: Identify terminal exons

Description

Usage

Arguments

Value